trying to debug on CI by abusing warnings lol

nwb_linkml/pyproject.toml

@@ -12,6 +12,9 @@ packages = [
     {include = "nwb_linkml", from="src"},
     #{include = "nwb_schema_language", from="../nwb_schema_language/src"}
 ]
+include = [
+    'src/nwb_linkml/schema/**/*'
+]
 
 
 [tool.poetry.dependencies]

nwb_linkml/src/nwb_linkml/__init__.py

@@ -1,3 +1,5 @@
 from nwb_linkml.monkeypatch import apply_patches
 apply_patches()
 
+from nwb_linkml.config import Config
+

nwb_linkml/src/nwb_linkml/config.py

@@ -2,8 +2,9 @@
 Manage the operation of nwb_linkml from environmental variables
 """
 import tempfile
+from typing import Any
 from pathlib import Path
-from pydantic import Field, DirectoryPath, computed_field, field_validator, FieldValidationInfo
+from pydantic import Field, DirectoryPath, computed_field, field_validator, model_validator, FieldValidationInfo
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 class Config(BaseSettings):
@@ -48,6 +49,15 @@ class Config(BaseSettings):
         assert v.exists()
         return v
 
+    @model_validator(mode='after')
+    def folder_exists(self) -> 'Config':
+        for field, path in self.model_dump().items():
+            if isinstance(path, Path):
+                path.mkdir(exist_ok=True, parents=True)
+                assert path.exists()
+        return self
+
+
     def __post_init__(self):
         self.cache_dir.mkdir(exist_ok=True)
         self.linkml_dir.mkdir(exist_ok=True)

nwb_linkml/tests/test_providers/test_provider_schema.py

@@ -4,6 +4,8 @@ import os
 import sys
 import warnings
 from pathlib import Path
+import yaml
+from pprint import pformat
 
 from typing import Optional, Union, List
 from ..fixtures import tmp_output_dir
@@ -13,6 +15,7 @@ import pytest
 from nwb_linkml.providers.schema import LinkMLProvider, PydanticProvider
 import nwb_linkml
 from nwb_linkml.maps.naming import version_module_case
+from nwb_linkml.providers.git import DEFAULT_REPOS
 
 
 CORE_MODULES = (
@@ -40,9 +43,9 @@ def test_linkml_provider(tmp_output_dir, repo_version, schema_version, schema_di
 
     provider = LinkMLProvider(path=tmp_output_dir, allow_repo=False)
     # clear any prior output
-    shutil.rmtree(provider.path, ignore_errors=True)
+    shutil.rmtree(provider.path)
     assert not provider.path.exists()
-    assert not provider.namespace_path('core', repo_version).exists()
+    assert not (provider.namespace_path('core', repo_version) / 'namespace.yaml').exists()
 
     # end to end, check that we can get the 'core' repo at the latest version
     # in the gitrepo
@@ -52,6 +55,30 @@ def test_linkml_provider(tmp_output_dir, repo_version, schema_version, schema_di
     assert all([mod in core.schema.imports for mod in CORE_MODULES])
     assert schema_dir in [path.name for path in (provider.path / 'core').iterdir()]
 
+def test_linkml_build_from_yaml(tmp_output_dir):
+    core = DEFAULT_REPOS['core']
+    git_dir = nwb_linkml.Config().git_dir / 'core'
+    if git_dir.exists():
+        shutil.rmtree(str(git_dir))
+    ns_file = core.provide_from_git('2.6.0')
+    assert git_dir.exists()
+    assert ns_file.exists()
+
+    # for the sake of debugging CI...
+    with open(ns_file) as nfile:
+        ns_yaml = yaml.safe_load(nfile)
+    warnings.warn(pformat(ns_yaml))
+    files = [str(f) for f in list(ns_file.parent.glob('*.yaml'))]
+    warnings.warn('\n'.join(files))
+
+    provider = LinkMLProvider(path=tmp_output_dir, allow_repo=False)
+
+    res = provider.build_from_yaml(ns_file)
+    warnings.warn(pformat(res))
+
+
+
+
 
 @pytest.mark.skip()
 @pytest.mark.depends(on=['test_linkml_provider'])